High Resolution Mapping of Function Elements in the Yeast Genome

描述(申请人提供)：真核DNA被包装成染色质，该染色质具有明确的组织结构。染色质是由核小体组成的，其在DNA上的位置决定了基因调控元件的可及性，最终决定了基因的表达水平。核小体通过许多机制受到高度调控，包括：翻译后修饰，伴侣促进的沉积和驱逐，以及染色质重塑复合体促进的重新定位。这种核小体状态通过与特定的基因调节蛋白相互作用来进一步调节基因的表达。核小体状态如何与基因调控因子相互作用在很大程度上是未知的，这是我们理解基因表达是如何在疾病中受到控制和错误调控的核心。在这里，我们建议通过首先在模型基因表达程序(热休克和产孢子)展开时以高分辨率绘制单个核小体状态的基因组位置来加深我们对该界面的理解。核小体状态的例子包括组蛋白修饰和核小体的定相、定位和宽度。其次，我们将通过检测当这些状态通过突变被消除时不会发生什么来确定这些状态对染色质组织和基因表达的贡献。第三，我们将创建与特定染色质和基因调控因子相互作用的高分辨率全基因组核小体图谱。这些目标旨在首先以高分辨率描述核小体状态的格局，然后确定它们的功能，然后主要使用酵母作为模型系统来确定它们与基因调控因子的相互作用。关键的核小体模式将在后生动物模型系统中进一步探索，以确定这些模式是否代表真核生物的基本原理。 公共卫生相关性：由于核小体的定位和调控在控制从酵母到人类的基因表达方面起着核心作用，而基因表达是正常和疾病细胞行为的根源，因此了解核小体的基因组组织状态是维持正确的细胞生理和纠正异常状态的关键。这个项目的目的是为了更好地了解核小体状态与基因表达的关系。

DESCRIPTION (provided by applicant): Eukaryotic DNA is packaged into chromatin, and this chromatin has a well-defined organization. Chromatin is composed of nucleosome building blocks, whose positioning along the DNA dictates the accessibility of gene regulatory elements, and ultimately the expression levels of genes. Nucleosomes are highly regulated through many mechanisms including: post-translational modifications, deposition and eviction that is facilitated by chaperones, and re-positioning facilitated by chromatin remodeling complexes. Such nucleosome states further regulate gene expression by interacting with specific gene regulatory proteins. How nucleosome states interface with gene regulatory factors is largely unknown and is central to our understanding of how gene expression is controlled and mis-regulated in diseases. Here, we propose to further our understanding of this interface by first mapping the genomic position of individual nucleosome states at high resolution as model gene expression programs (heat shock and sporulation) unfold. Examples of nucleosome states include histone modifications, and nucleosome phasing, positioning, and width. Second, we will ascertain the contribution of such states to chromatin organization and gene expression, by examining what fails to happen when such states are eliminated through mutagenesis. Third, we will create high-resolution genome-wide maps of nucleosomes that interact with specific chromatin and gene regulatory factors. These aims are intended to first describe the landscape of nucleosomal states at high resolution, then identify their function, and then ascertain their interplay with gene regulatory factors using primarily Saccharomyces as a model system.Key nucleosomal patterns will be further explored in metazoan model systems, to ascertain whether such patterns represent fundamental principles in eukaryotes. PUBLIC HEALTH RELEVANCE: Since nucleosome positioning and regulation play central roles in controlling gene expression from yeast to man, and gene expression is the origin of both normal and diseased cellular behavior, knowledge of the genomic organizational state of nucleosomes is key toward maintaining proper cell physiology and rectifying aberrant states. This project is intended to provide a greater understanding of nucleosomal states in relation to gene expression.